bioRxiv preprint doi: https://doi.org/10.1101/2020.07.01.182659; this version posted July 1, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. High affinity binding of SARS-CoV-2 spike protein enhances ACE2 carboxypeptidase activity Jinghua Lu and Peter D. Sun Structural Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, Rockville, Maryland 20852 Corresponding author email: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.01.182659; this version posted July 1, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. Abstract A novel coronavirus (SARS-CoV-2) has emerged to a global pandemic and caused significant damages to public health. Human angiotensin-converting enzyme 2(ACE2) was identified as the entry receptor for SARS-CoV-2. As a carboxypeptidase, ACE2 cleaves many biological substrates besides Ang II to control vasodilatation and permeability. Given the nanomolar high affinity between ACE2 and SARS-CoV-2 spike protein, we wonder how this interaction would affect the enzymatic activity of ACE2. Surprisingly, SARS-CoV-2 trimeric spike protein increased ACE2 proteolytic activity ~3-10 fold when fluorogenic caspase-1 substrate and Bradykinin-analog peptides were used to characterize ACE2 activity. In addition, the enhancement was mediated by ACE2 binding of RBD domain of SARS-CoV-2 spike. These results highlighted the altered activity of ACE2 during SARS-CoV-2 infection and would shed new lights on the pathogenesis of COVID-19 and its complications for better treatments. 2 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.01.182659; this version posted July 1, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. Introduction The novel coronavirus SARS-CoV-2 has emerged as an unprecedented global pandemic 1, 2, 3 and as of June 8, 2020, there are nearly 7 million confirmed cases worldwide, leading to 400,857 deaths(WHO). The infection of SARS-CoV-2 causes fever, dry cough, severe respiratory illness and pneumonia, a disease recently named COVID-194. Pathological studies have revealed all features of diffuse alveolar damage (DAD) with excessive fluid in the lungs and critically ill patients often need ventilators to support oxygen. Furthermore, a frequent complication of COVID-19 that blood clotted abnormally is observed in many hospitalized patients5. Therefore, there is an urgent need for a mechanistic understanding of the pathogenicity of SARS-CoV-2 and its concomitant complications to be able to treat hospitalized patients. During the sudden emergency and rapid spread of SARS-CoV-2, global efforts have identified human angiotensin-converting enzyme 2(ACE2) as the entry receptor for this new coronavirus2, which was also the entry receptor for SARS-CoV6, 7, 8. Structural studies revealed that SARS-CoV-2 spike (S) glycoprotein binds ACE2 with higher affinity (~15-40nM) than SARS-CoV spike protein9, 10, 11, 12. The overall structure of SARS-CoV-2 S resembles that of SARS-CoV S with the RBD domain of one protomer in spike protein trimer tightly interacting ACE2 extracellular enzymatic domain. Physiologically, ACE2 is a zinc metalloprotease (carboxypeptidase), a homolog to dipeptidase angiotensin-converting enzyme (ACE) but with different substrate specificity 13. ACE cleaves the C-terminal dipeptide from Ang I to produce the potent vasopressor octapeptide Ang II, whereas ACE2 further cleaves the carboxyl- terminus to produce Ang 1-7 to deactivate Ang II. Therefore, ACE and ACE2 together play important roles in regulating vasoconstriction and vasodilatation in the rennin-angiotensin system (RAS). In the meanwhile, ACE and ACE2 plays critical role in kinin-kallikrein system to control vascular permeability and vasodilatation14. ACE deactivates Bradykinin nonapeptide, the ligand for constitutively expressed bradykinin receptor B2. Bradykinin can be further processed by carboxypeptidase N or M to form des- Arg9-bradykinin, which is a potent ligand for inflammation-inducible bradykinin receptor B115. Beyond Renin-angiotensin and kinin-kallikrein systems, ACE2 also cleaves other biological peptides such as Apelin-13 that activates apelin receptor to cause vasodilatation. However, there is limited information on the level of these substrates during SARS-CoV-2 infection given the fact that ACE2 is the major entry receptor for this new coronavirus. Compared to relatively low expression of ACE, ACE2 is predominantly expressed in the lung on pneumocytes II, which explains that lung is the major organ infected by SARS-CoV-2. Critical clinical observations showed that COVID-19 patients often had dyspnea and accumulation of fluid in the lungs representing local angioedema, which clearly suggests the pathological involvement of vascular 3 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.01.182659; this version posted July 1, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. permeability and vasodilatation during SARS-CoV-2 infection. However, there was no direct assessment of ACE2 enzymatic activity during coronavirus infection. Here we examined how the binding of SARS- CoV-2 spike protein would affect the intrinsic enzymatic activity of ACE2 using one well characterized fluorogenic ACE2 substrate, the caspase-1 substrate (Mca-YVADAPK-Dnp)13. In comparison, ACE substrate, a bradykinin analog (Mca-RPPGFSAFK-Dnp) was also included in the enzymatic activity assessment16. To our surprise, SARS-CoV-2 spike enhanced ACE2 proteolytic activity to cleave Mca- YVADAPK-Dnp, which was mediated by ACE2 binding of RBD. Furthermore, SARS-CoV-2 RBD enhanced ACE2 activity to hydrolyze the bradykinin-analog better than SARS-CoV RBD. Measurements of kinetic constants also showed that SARS-CoV-2 spike protein altered the binding affinity (Km) of ACE2 to the caspase-1 substrate or Bradykinin-analog. We propose that this new line of evidence that SARS-CoV-2 spike protein significantly alters ACE2 activity and specificity could be clinically relevant to the understanding of the pathogenesis of COVID-19. 4 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.01.182659; this version posted July 1, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. Results SARS-CoV-2 spike protein enhances ACE2 activity Genetic analysis revealed that SARS-CoV-2 was highly homologous to severe acute respiratory syndrome coronavirus (SARS-CoV) that infected human cells with angiotensin-converting enzyme 2(ACE2) receptor2, 8. After the outbreak of COVID-19, ACE2 was quickly identified as the entry receptor for SAR- Cov-2 as well. Further structural studies demonstrated that both SARS-CoV-2 and SARS-CoV utilized their RBD domain to interact with ACE2 at a very similar binding mode. However, SARS-CoV-2 spike protein displays a much higher binding affinity to ACE2 compared with SARS-CoV. Given the nanomolar affinity between ACE2 and SARS-CoV-2 S spike protein, we wonder how the binding of SARS-CoV-2 spike protein to ACE2 would affect its enzymatic activity since ACE2 is a critical component in both the Rennin-angiotensin and Kinin-kallikrein system as a carboxypeptidase14, 17. As previously reported, ACE2 efficiently hydrolyzes biological peptides with a consensus sequence of Pro-X(1-3 residues)-Pro-hydrophobic at P5-P1’ positions13, with cleavage between proline and the hydrophobic residue as exemplified by Ang II (DRVYIHP↓F) and des-Arg9-BK (RPPGFSP↓F). ACE2 also cleaves peptides with a basic residue at P1’ position such as Dynorphin A (YGGFLRRIRPKL↓K) and Neurotensin 1-8(pE-LYENKP↓R). To rapidly and continuously assess enzyme activity, fluorogenic peptide substrates were normally used. Therefore, we monitored ACE2 proteolytic activity by measuring the degradation of fluorogenic capase-1 substrate Mca-YVADAPK(Dnp)13. In addition, a bradykinin derivative Mca-RPPGFSAFK(Dnp)-OH16 that was developed as endothelin-Converting enzyme-1 (ECE1) and ACE substrate was also analyzed.. Indeed, ACE2 efficiently hydrolyzed Mca-YVADAPK(Dnp) but cleaved bradykinin analog Mca-RPPGFSAFK(Dnp)-OH less (Figure 1 A and B). Within 2 hours, the cleavage of Mca-YVADAPK (Dnp) by ACE2 produced 20,000 relative fluorescence units (RFU), whereas the cleavage of Mca-RPPGFSAFK(Dnp)-OH by ACE2 produced 2000 RFU. Surprisingly, the addition of SARS-CoV-2 spike protein at 14ug/ml concentration to the enzymatic assays significantly enhanced ACE2 proteolytic activity. Within 2 hours, the hydrolysis of Mca-YVADAPK(Dnp) by ACE2 produced ~70,000 RFU in the presence of SARS-CoV-2 spike protein (Figure 1A). Similarly, SARS- CoV-2 spike protein enhanced ACE2 cleavage of bradykinin analog Mca-RPPGFSAFK(Dnp)-OH to produce ~3 times more RFU within 2 hours (Figure 1B). Previous enzymatic assays showed that ACE2 activity increased with the concentrations of NaCl between 0.15M to 1M. We then carried out the same enzymatic assays at increased concentration of NaCl. Consistently, SARS-CoV-2 spike protein enhanced ACE2 activity at 0.3M and 1M NaCl and enabled ACE2 to cleave bradykinin-analog as well 5 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.01.182659; this version posted July 1, 2020.